library(multiMiR)
## Welcome to multiMiR.
## 
## multiMiR database URL has been set to the 
## default value: http://multimir.org/
## 
## Database Version: 2.3.0  Updated: 2020-04-15
library(clusterProfiler)
## 
## clusterProfiler v4.12.2 Learn more at https://yulab-smu.top/contribution-knowledge-mining/
## 
## Please cite:
## 
## T Wu, E Hu, S Xu, M Chen, P Guo, Z Dai, T Feng, L Zhou, W Tang, L Zhan,
## X Fu, S Liu, X Bo, and G Yu. clusterProfiler 4.0: A universal
## enrichment tool for interpreting omics data. The Innovation. 2021,
## 2(3):100141
## 
## Attaching package: 'clusterProfiler'
## The following object is masked from 'package:multiMiR':
## 
##     select
## The following object is masked from 'package:stats':
## 
##     filter
library(org.Hs.eg.db)
## Loading required package: AnnotationDbi
## Loading required package: stats4
## Loading required package: BiocGenerics
## 
## Attaching package: 'BiocGenerics'
## The following objects are masked from 'package:stats':
## 
##     IQR, mad, sd, var, xtabs
## The following objects are masked from 'package:base':
## 
##     anyDuplicated, aperm, append, as.data.frame, basename, cbind,
##     colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
##     get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
##     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
##     Position, rank, rbind, Reduce, rownames, sapply, setdiff, table,
##     tapply, union, unique, unsplit, which.max, which.min
## Loading required package: Biobase
## Welcome to Bioconductor
## 
##     Vignettes contain introductory material; view with
##     'browseVignettes()'. To cite Bioconductor, see
##     'citation("Biobase")', and for packages 'citation("pkgname")'.
## Loading required package: IRanges
## Loading required package: S4Vectors
## 
## Attaching package: 'S4Vectors'
## The following object is masked from 'package:clusterProfiler':
## 
##     rename
## The following object is masked from 'package:utils':
## 
##     findMatches
## The following objects are masked from 'package:base':
## 
##     expand.grid, I, unname
## 
## Attaching package: 'IRanges'
## The following object is masked from 'package:clusterProfiler':
## 
##     slice
## The following object is masked from 'package:grDevices':
## 
##     windows
## 
## Attaching package: 'AnnotationDbi'
## The following object is masked from 'package:clusterProfiler':
## 
##     select
## 
library(stringr)
library(ggplot2)

0. Loading of Results

A. List of all Gene names in the dataset

gene.names = readRDS("data/derived/unique_gene_names.rds")

B. Selected Features

results.glmnet.cox = readRDS("data/sel_features/results_glmnet_cox_coef_1se.rds")
sel.features = results.glmnet.cox
sel.features
## $fold3
## $fold3$elasticnet_0.5
## $fold3$elasticnet_0.5$dev
##  hsa-mir-101-2   hsa-mir-125a   hsa-mir-1277   hsa-mir-1307   hsa-mir-130b 
##   -0.143780726   -0.134165336   -0.448077046    0.373110532    0.106986296 
## hsa-mir-199a-2   hsa-mir-199b    hsa-mir-29c hsa-mir-3199-1 hsa-mir-320c-2 
##    0.127672251    0.237477836   -0.051799128   -0.081638106   -0.267066343 
##   hsa-mir-3923   hsa-mir-513b    hsa-mir-605    hsa-mir-664    hsa-mir-7-1 
##    0.147642241   -0.053475381   -0.073428752   -0.940570385    0.539530827 
##    MRE11A.R2Gn      AKT1.R2Gn     RAD51.R2Gn     MAPK9.R2Gn     MAPK3.R2Gn 
##    0.027384525   -0.015780032    0.479477264   -0.085717111   -0.634308840 
##     STMN1.R2Gn     CHEK1.R2Gn      CDK1.R2Gn     EEF2K.R2Gn      TYMS.R2Gn 
##    0.006983371    0.622267874    0.185459762   -0.300795892    0.131317104 
##     FOXM1.R2Gn      XIAP.R2Gn     PREX1.R2Gn       RET.R2Gn      TFRC.RPPA 
##    0.576229539   -1.263779736   -0.074469173    0.020331914    0.081977399 
##        CLDN7.g        ANXA1.g 
##   -0.009327215    0.211844775 
## 
## $fold3$elasticnet_0.5$c
##   hsa-mir-1307   hsa-mir-130b   hsa-mir-199b hsa-mir-320c-2   hsa-mir-3923 
##    0.032348699    0.168954949    0.120611119   -0.130133354    0.113022189 
##   hsa-mir-513b    hsa-mir-605    hsa-mir-664    hsa-mir-7-1     RAD51.R2Gn 
##   -0.089747704   -0.021615310   -0.941792954    0.095432953    0.227265782 
##     MAPK9.R2Gn     MAPK3.R2Gn     CHEK1.R2Gn      CDK1.R2Gn     EEF2K.R2Gn 
##   -0.060114359   -0.450152165    0.146994963    0.218645287   -0.109938413 
##      TYMS.R2Gn     FOXM1.R2Gn      XIAP.R2Gn     PREX1.R2Gn      TFRC.RPPA 
##    0.002027408    0.533289744   -0.865276041   -0.009236919    0.052186205 
##        ANXA1.g 
##    0.067016750 
## 
## 
## $fold3$lasso
## $fold3$lasso$dev
##  hsa-mir-3923   hsa-mir-664    MAPK3.R2Gn    FOXM1.R2Gn     XIAP.R2Gn 
##  0.0283139242 -1.7119840992 -0.0302255060  0.9724083977 -0.4313080991 
##     TFRC.RPPA 
##  0.0006765457 
## 
## $fold3$lasso$c
## hsa-mir-320c-2   hsa-mir-3923    hsa-mir-664     MAPK3.R2Gn     FOXM1.R2Gn 
##    -0.01983995     0.05010126    -1.68127653    -0.20066173     1.01943349 
##      XIAP.R2Gn      TFRC.RPPA 
##    -0.68680559     0.01437263 
## 
## 
## 
## $fold5
## $fold5$elasticnet_0.5
## $fold5$elasticnet_0.5$dev
## numeric(0)
## 
## $fold5$elasticnet_0.5$c
## hsa-mir-3923 hsa-mir-513b  hsa-mir-664    CDK1.R2Gn   FOXM1.R2Gn    XIAP.R2Gn 
##   0.04319868  -0.02301522  -0.69523526   0.08450855   0.31735481  -0.17014923 
## 
## 
## $fold5$lasso
## $fold5$lasso$dev
##  hsa-mir-3923   hsa-mir-664    MAPK3.R2Gn    FOXM1.R2Gn     XIAP.R2Gn 
##  0.0283139242 -1.7119840992 -0.0302255060  0.9724083977 -0.4313080991 
##     TFRC.RPPA 
##  0.0006765457 
## 
## $fold5$lasso$c
##   hsa-mir-1277   hsa-mir-199b hsa-mir-3199-1 hsa-mir-320c-2    hsa-mir-330 
##    -2.88038031     0.92158572    -0.17472735    -1.85934550     0.18559755 
##   hsa-mir-3912   hsa-mir-3923    hsa-mir-605    hsa-mir-659    hsa-mir-7-1 
##    -1.17464142     0.74720999    -0.47819460    -0.43076862     5.75707121 
##    hsa-mir-873     PRKCD.R2Gn      AKT1.R2Gn     MAPK3.R2Gn     WWTR1.R2Gn 
##    -0.16866896    -0.02331865    -0.03815669    -0.30593369     0.86778659 
##      TYMS.R2Gn     FOXM1.R2Gn      XIAP.R2Gn     PREX1.R2Gn       RET.R2Gn 
##     1.00291281     1.19640658    -8.39856593    -0.44355829     2.35899817 
##      TFRC.RPPA        CLDN7.g        ANXA1.g 
##     0.48479251    -0.10295925     1.02489560 
## 
## 
## 
## $fold10
## $fold10$elasticnet_0.5
## $fold10$elasticnet_0.5$dev
##  hsa-mir-101-2   hsa-mir-125a   hsa-mir-1277   hsa-mir-1307   hsa-mir-130b 
##   -0.005171816   -0.049259334   -0.147024699    0.204188473    0.151588631 
## hsa-mir-199a-2   hsa-mir-199b    hsa-mir-29c hsa-mir-3199-1 hsa-mir-320c-2 
##    0.046253821    0.168289112   -0.006928248   -0.020207702   -0.192228371 
##   hsa-mir-3923   hsa-mir-513b    hsa-mir-605    hsa-mir-664    hsa-mir-7-1 
##    0.127817926   -0.078976945   -0.050266895   -0.948916208    0.286021290 
##     RAD51.R2Gn     MAPK9.R2Gn     MAPK3.R2Gn     CHEK1.R2Gn      CDK1.R2Gn 
##    0.342007316   -0.076544205   -0.542538844    0.375489918    0.208250895 
##     EEF2K.R2Gn      TYMS.R2Gn     FOXM1.R2Gn      XIAP.R2Gn     PREX1.R2Gn 
##   -0.207113324    0.060684819    0.561982342   -1.056246305   -0.044114455 
##      TFRC.RPPA        ANXA1.g 
##    0.067949608    0.134325304 
## 
## $fold10$elasticnet_0.5$c
##  hsa-mir-101-2   hsa-mir-125a   hsa-mir-1277   hsa-mir-1307   hsa-mir-130b 
##   -0.077056038   -0.095520457   -0.304152528    0.296516093    0.130758687 
## hsa-mir-199a-2   hsa-mir-199b    hsa-mir-29c hsa-mir-3199-1 hsa-mir-320c-2 
##    0.086497506    0.202242747   -0.025770943   -0.053535040   -0.229808987 
##   hsa-mir-3923   hsa-mir-513b    hsa-mir-605    hsa-mir-664    hsa-mir-7-1 
##    0.137474912   -0.065633768   -0.062185080   -0.949567413    0.412663607 
##     RAD51.R2Gn     MAPK9.R2Gn     MAPK3.R2Gn     STMN1.R2Gn     CHEK1.R2Gn 
##    0.414282319   -0.078992679   -0.592334904    0.001022566    0.514261747 
##      CDK1.R2Gn     EEF2K.R2Gn      TYMS.R2Gn     FOXM1.R2Gn      XIAP.R2Gn 
##    0.197959917   -0.255114112    0.096943992    0.571893341   -1.166807581 
##     PREX1.R2Gn      TFRC.RPPA        ANXA1.g 
##   -0.058933193    0.075364992    0.174931429 
## 
## 
## $fold10$lasso
## $fold10$lasso$dev
## hsa-mir-320c-2   hsa-mir-3923    hsa-mir-664     MAPK3.R2Gn     FOXM1.R2Gn 
##    -0.05949828     0.06474545    -1.65685970    -0.33221861     1.06976637 
##      XIAP.R2Gn      TFRC.RPPA 
##    -0.91478154     0.02745507 
## 
## $fold10$lasso$c
##  hsa-mir-664   FOXM1.R2Gn 
## -0.415606866  0.007135668

1. Convert microRNA to genes

Also remove the ending “.R2Gn” and “.RPPA” from gene names.

split.by.omic = function(variable.list) {
  out.mRSG = variable.list[startsWith(variable.list, "hsa")]
  out.R2Gn = variable.list[endsWith(variable.list, ".R2Gn")]
  out.RPPA = variable.list[endsWith(variable.list, ".RPPA")]
  #Mutations and gistict for glmnet only
  out.M = variable.list[endsWith(variable.list, ".M")] 
  out.g = variable.list[endsWith(variable.list, ".g")] 
  out = list("miRNASeqGene" = out.mRSG,
             "RNASeq2GeneNorm" = out.R2Gn,
             "RPPAArray" = out.RPPA,
             "Mutations" = out.M,
             "gistict" = out.g)
  out
}
multiomics.to.GENES = function(sel.features, full.search = F, table = "validated", drop.miRNA = F) {
  multiomics.list = split.by.omic(sel.features)
  # Convert miRNASeqGene to target GENE names
  # Skipped and returns an empty list instead of the list of select features,
  # or if microRNA features are explicitly dropped (drop.miRNA = T).
  # (Usually done when the features has only a few miRNA and unable to target any genes)
  if (length(multiomics.list[[1]]) > 0 & !drop.miRNA) {
    if (!full.search) { # Search only among the 198 genes in ACC, recommended
    targets= get_multimir(mirna = multiomics.list[[1]], 
                          target = gene.names,
                          table = table,
                          summary = T)
    mRSG.target.genes = unique(targets@data$target_symbol)
    } else { # Search the full dataset, not recommended. 
             # Use only if ACC gene search returns nothing or fails.
             # Genes not in the ACC genes need to be manually removed.
    targets= get_multimir(mirna = multiomics.list[[1]], 
                          table = table,
                          summary = T)  
    mRSG.target.genes = unique(targets@data$target_symbol)
    }
    
  } else {
    mRSG.target.genes = list()
  }
  #Remove suffix for Pathway Analysis Compatibility
  R2Gn.genes = str_remove(multiomics.list[[2]], ".R2Gn")
  
  RPPA.genes = str_remove(multiomics.list[[3]], ".RPPA")
  
  M.genes = str_remove(multiomics.list[[4]], ".M")
  
  g.genes = str_remove(multiomics.list[[5]], ".g")
  
  #Join all cleaned-up genes are remove duplicates.
  out1 = c(mRSG.target.genes, R2Gn.genes, RPPA.genes, M.genes, g.genes)
  out = as.character(unique(out1))
  out
}

All microRNAs are dropped as they do not contribute enough to convert to genes.

geneNames <- list("3F_0.5_DEV"= multiomics.to.GENES(names(sel.features$fold3$elasticnet_0.5$dev), drop.miRNA = T),
                  "3F_0.5_C"= multiomics.to.GENES(names(sel.features$fold3$elasticnet_0.5$c), drop.miRNA = T),
                  "3F_1_DEV"= multiomics.to.GENES(names(sel.features$fold3$lasso$dev), drop.miRNA = T),
                  "3F_1_C"= multiomics.to.GENES(names(sel.features$fold3$lasso$c), drop.miRNA = T),
                  #"5F_0.5_DEV"= multiomics.to.GENES(names(sel.features$fold5$elasticnet_0.5$dev)), # 0 variables selected
                  "5F_0.5_C"= multiomics.to.GENES(names(sel.features$fold5$elasticnet_0.5$c), drop.miRNA = T),
                  "5F_1_DEV"=multiomics.to.GENES(names(sel.features$fold5$lasso$dev), drop.miRNA = T),
                  "5F_1_C"= multiomics.to.GENES(names(sel.features$fold5$lasso$c), drop.miRNA = T),
                  "10F_0.5_DEV"= multiomics.to.GENES(names(sel.features$fold10$elasticnet_0.5$dev), drop.miRNA = T),
                  "10F_0.5_C"= multiomics.to.GENES(names(sel.features$fold10$elasticnet_0.5$c), drop.miRNA = T),
                  "10F_1_DEV"= multiomics.to.GENES(names(sel.features$fold10$lasso$dev), drop.miRNA = T),
                  "10F_1_C"= multiomics.to.GENES(names(sel.features$fold10$lasso$c), drop.miRNA = T)
                  )
geneNames
## $`3F_0.5_DEV`
##  [1] "MRE11A" "AKT1"   "RAD51"  "MAPK9"  "MAPK3"  "STMN1"  "CHEK1"  "CDK1"  
##  [9] "EEF2K"  "TYMS"   "FOXM1"  "XIAP"   "PREX1"  "RET"    "TFRC"   "CLDN7" 
## [17] "ANXA1" 
## 
## $`3F_0.5_C`
##  [1] "RAD51" "MAPK9" "MAPK3" "CHEK1" "CDK1"  "EEF2K" "TYMS"  "FOXM1" "XIAP" 
## [10] "PREX1" "TFRC"  "ANXA1"
## 
## $`3F_1_DEV`
## [1] "MAPK3" "FOXM1" "XIAP"  "TFRC" 
## 
## $`3F_1_C`
## [1] "MAPK3" "FOXM1" "XIAP"  "TFRC" 
## 
## $`5F_0.5_C`
## [1] "CDK1"  "FOXM1" "XIAP" 
## 
## $`5F_1_DEV`
## [1] "MAPK3" "FOXM1" "XIAP"  "TFRC" 
## 
## $`5F_1_C`
##  [1] "PRKCD" "AKT1"  "MAPK3" "WWTR1" "TYMS"  "FOXM1" "XIAP"  "PREX1" "RET"  
## [10] "TFRC"  "CLDN7" "ANXA1"
## 
## $`10F_0.5_DEV`
##  [1] "RAD51" "MAPK9" "MAPK3" "CHEK1" "CDK1"  "EEF2K" "TYMS"  "FOXM1" "XIAP" 
## [10] "PREX1" "TFRC"  "ANXA1"
## 
## $`10F_0.5_C`
##  [1] "RAD51" "MAPK9" "MAPK3" "STMN1" "CHEK1" "CDK1"  "EEF2K" "TYMS"  "FOXM1"
## [10] "XIAP"  "PREX1" "TFRC"  "ANXA1"
## 
## $`10F_1_DEV`
## [1] "MAPK3" "FOXM1" "XIAP"  "TFRC" 
## 
## $`10F_1_C`
## [1] "FOXM1"
saveRDS(geneNames, file = "data/sel_features/gene_converted/genes_glmnet_cox_1se.rds")

2. Pathway Analysis

A. GO Classification

ggo_MF <- list()#functional profile of a geneset for Molecular Function
ggo_BP <- list()#functional profile of a geneset for Biological Process
ggo_CC <- list()#functional profile of a geneset for Cellular Component


for(z in 1:length(geneNames)){
  print(z)
  input <- geneNames[[z]]

  ggo_MF[[z]] <- groupGO(gene=input,
    OrgDb = org.Hs.eg.db,
    ont="MF",
    keyType="SYMBOL",
    readable=TRUE)
  
  ggo_BP[[z]] <- groupGO(gene=input,
    OrgDb = org.Hs.eg.db,
    ont="BP",
    keyType="SYMBOL",
    readable=TRUE)

  ggo_CC[[z]] <- groupGO(gene=input,
    OrgDb = org.Hs.eg.db,
    ont="CC",
    keyType="SYMBOL",
    readable=TRUE)    
}
## [1] 1
## [1] 2
## [1] 3
## [1] 4
## [1] 5
## [1] 6
## [1] 7
## [1] 8
## [1] 9
## [1] 10
## [1] 11
for(z in 1:length(geneNames)) {
  print(head(ggo_MF[[z]]))
  print(head(ggo_BP[[z]]))
  print(head(ggo_CC[[z]]))
}
##                    ID                  Description Count GeneRatio
## GO:0003774 GO:0003774  cytoskeletal motor activity     0      0/17
## GO:0003824 GO:0003824           catalytic activity    10     10/17
## GO:0005198 GO:0005198 structural molecule activity     1      1/17
## GO:0005215 GO:0005215         transporter activity     0      0/17
## GO:0005488 GO:0005488                      binding    16     16/17
## GO:0009055 GO:0009055   electron transfer activity     0      0/17
##                                                                                              geneID
## GO:0003774                                                                                         
## GO:0003824                                    AKT1/RAD51/MAPK9/MAPK3/CHEK1/CDK1/EEF2K/TYMS/XIAP/RET
## GO:0005198                                                                                    CLDN7
## GO:0005215                                                                                         
## GO:0005488 AKT1/RAD51/MAPK9/MAPK3/STMN1/CHEK1/CDK1/EEF2K/TYMS/FOXM1/XIAP/PREX1/RET/TFRC/CLDN7/ANXA1
## GO:0009055                                                                                         
##                    ID           Description Count GeneRatio
## GO:0000003 GO:0000003          reproduction     3      3/17
## GO:0002376 GO:0002376 immune system process     8      8/17
## GO:0008152 GO:0008152     metabolic process    14     14/17
## GO:0009987 GO:0009987      cellular process    16     16/17
## GO:0016032 GO:0016032         viral process     3      3/17
## GO:0022414 GO:0022414  reproductive process     3      3/17
##                                                                                              geneID
## GO:0000003                                                                          AKT1/RAD51/CDK1
## GO:0002376                                               AKT1/MAPK9/MAPK3/XIAP/PREX1/RET/TFRC/ANXA1
## GO:0008152             AKT1/RAD51/MAPK9/MAPK3/CHEK1/CDK1/EEF2K/TYMS/FOXM1/XIAP/PREX1/RET/TFRC/ANXA1
## GO:0009987 AKT1/RAD51/MAPK9/MAPK3/STMN1/CHEK1/CDK1/EEF2K/TYMS/FOXM1/XIAP/PREX1/RET/TFRC/CLDN7/ANXA1
## GO:0016032                                                                           AKT1/CDK1/TFRC
## GO:0022414                                                                          AKT1/RAD51/CDK1
##                    ID                Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex     7      7/17
## GO:0044423 GO:0044423           virion component     0      0/17
## GO:0110165 GO:0110165 cellular anatomical entity    16     16/17
##                                                                                              geneID
## GO:0032991                                                     AKT1/RAD51/CHEK1/CDK1/FOXM1/RET/TFRC
## GO:0044423                                                                                         
## GO:0110165 AKT1/RAD51/MAPK9/MAPK3/STMN1/CHEK1/CDK1/EEF2K/TYMS/FOXM1/XIAP/PREX1/RET/TFRC/CLDN7/ANXA1
##                    ID                  Description Count GeneRatio
## GO:0003774 GO:0003774  cytoskeletal motor activity     0      0/12
## GO:0003824 GO:0003824           catalytic activity     8      8/12
## GO:0005198 GO:0005198 structural molecule activity     0      0/12
## GO:0005215 GO:0005215         transporter activity     0      0/12
## GO:0005488 GO:0005488                      binding    12     12/12
## GO:0009055 GO:0009055   electron transfer activity     0      0/12
##                                                                         geneID
## GO:0003774                                                                    
## GO:0003824                        RAD51/MAPK9/MAPK3/CHEK1/CDK1/EEF2K/TYMS/XIAP
## GO:0005198                                                                    
## GO:0005215                                                                    
## GO:0005488 RAD51/MAPK9/MAPK3/CHEK1/CDK1/EEF2K/TYMS/FOXM1/XIAP/PREX1/TFRC/ANXA1
## GO:0009055                                                                    
##                    ID           Description Count GeneRatio
## GO:0000003 GO:0000003          reproduction     2      2/12
## GO:0002376 GO:0002376 immune system process     6      6/12
## GO:0008152 GO:0008152     metabolic process    12     12/12
## GO:0009987 GO:0009987      cellular process    12     12/12
## GO:0016032 GO:0016032         viral process     2      2/12
## GO:0022414 GO:0022414  reproductive process     2      2/12
##                                                                         geneID
## GO:0000003                                                          RAD51/CDK1
## GO:0002376                                   MAPK9/MAPK3/XIAP/PREX1/TFRC/ANXA1
## GO:0008152 RAD51/MAPK9/MAPK3/CHEK1/CDK1/EEF2K/TYMS/FOXM1/XIAP/PREX1/TFRC/ANXA1
## GO:0009987 RAD51/MAPK9/MAPK3/CHEK1/CDK1/EEF2K/TYMS/FOXM1/XIAP/PREX1/TFRC/ANXA1
## GO:0016032                                                           CDK1/TFRC
## GO:0022414                                                          RAD51/CDK1
##                    ID                Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex     5      5/12
## GO:0044423 GO:0044423           virion component     0      0/12
## GO:0110165 GO:0110165 cellular anatomical entity    12     12/12
##                                                                         geneID
## GO:0032991                                         RAD51/CHEK1/CDK1/FOXM1/TFRC
## GO:0044423                                                                    
## GO:0110165 RAD51/MAPK9/MAPK3/CHEK1/CDK1/EEF2K/TYMS/FOXM1/XIAP/PREX1/TFRC/ANXA1
##                    ID                  Description Count GeneRatio
## GO:0003774 GO:0003774  cytoskeletal motor activity     0       0/4
## GO:0003824 GO:0003824           catalytic activity     2       2/4
## GO:0005198 GO:0005198 structural molecule activity     0       0/4
## GO:0005215 GO:0005215         transporter activity     0       0/4
## GO:0005488 GO:0005488                      binding     4       4/4
## GO:0009055 GO:0009055   electron transfer activity     0       0/4
##                           geneID
## GO:0003774                      
## GO:0003824            MAPK3/XIAP
## GO:0005198                      
## GO:0005215                      
## GO:0005488 MAPK3/FOXM1/XIAP/TFRC
## GO:0009055                      
##                    ID           Description Count GeneRatio
## GO:0000003 GO:0000003          reproduction     0       0/4
## GO:0002376 GO:0002376 immune system process     3       3/4
## GO:0008152 GO:0008152     metabolic process     4       4/4
## GO:0009987 GO:0009987      cellular process     4       4/4
## GO:0016032 GO:0016032         viral process     1       1/4
## GO:0022414 GO:0022414  reproductive process     0       0/4
##                           geneID
## GO:0000003                      
## GO:0002376       MAPK3/XIAP/TFRC
## GO:0008152 MAPK3/FOXM1/XIAP/TFRC
## GO:0009987 MAPK3/FOXM1/XIAP/TFRC
## GO:0016032                  TFRC
## GO:0022414                      
##                    ID                Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex     2       2/4
## GO:0044423 GO:0044423           virion component     0       0/4
## GO:0110165 GO:0110165 cellular anatomical entity     4       4/4
##                           geneID
## GO:0032991            FOXM1/TFRC
## GO:0044423                      
## GO:0110165 MAPK3/FOXM1/XIAP/TFRC
##                    ID                  Description Count GeneRatio
## GO:0003774 GO:0003774  cytoskeletal motor activity     0       0/4
## GO:0003824 GO:0003824           catalytic activity     2       2/4
## GO:0005198 GO:0005198 structural molecule activity     0       0/4
## GO:0005215 GO:0005215         transporter activity     0       0/4
## GO:0005488 GO:0005488                      binding     4       4/4
## GO:0009055 GO:0009055   electron transfer activity     0       0/4
##                           geneID
## GO:0003774                      
## GO:0003824            MAPK3/XIAP
## GO:0005198                      
## GO:0005215                      
## GO:0005488 MAPK3/FOXM1/XIAP/TFRC
## GO:0009055                      
##                    ID           Description Count GeneRatio
## GO:0000003 GO:0000003          reproduction     0       0/4
## GO:0002376 GO:0002376 immune system process     3       3/4
## GO:0008152 GO:0008152     metabolic process     4       4/4
## GO:0009987 GO:0009987      cellular process     4       4/4
## GO:0016032 GO:0016032         viral process     1       1/4
## GO:0022414 GO:0022414  reproductive process     0       0/4
##                           geneID
## GO:0000003                      
## GO:0002376       MAPK3/XIAP/TFRC
## GO:0008152 MAPK3/FOXM1/XIAP/TFRC
## GO:0009987 MAPK3/FOXM1/XIAP/TFRC
## GO:0016032                  TFRC
## GO:0022414                      
##                    ID                Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex     2       2/4
## GO:0044423 GO:0044423           virion component     0       0/4
## GO:0110165 GO:0110165 cellular anatomical entity     4       4/4
##                           geneID
## GO:0032991            FOXM1/TFRC
## GO:0044423                      
## GO:0110165 MAPK3/FOXM1/XIAP/TFRC
##                    ID                  Description Count GeneRatio
## GO:0003774 GO:0003774  cytoskeletal motor activity     0       0/3
## GO:0003824 GO:0003824           catalytic activity     2       2/3
## GO:0005198 GO:0005198 structural molecule activity     0       0/3
## GO:0005215 GO:0005215         transporter activity     0       0/3
## GO:0005488 GO:0005488                      binding     3       3/3
## GO:0009055 GO:0009055   electron transfer activity     0       0/3
##                     geneID
## GO:0003774                
## GO:0003824       CDK1/XIAP
## GO:0005198                
## GO:0005215                
## GO:0005488 CDK1/FOXM1/XIAP
## GO:0009055                
##                    ID           Description Count GeneRatio          geneID
## GO:0000003 GO:0000003          reproduction     1       1/3            CDK1
## GO:0002376 GO:0002376 immune system process     1       1/3            XIAP
## GO:0008152 GO:0008152     metabolic process     3       3/3 CDK1/FOXM1/XIAP
## GO:0009987 GO:0009987      cellular process     3       3/3 CDK1/FOXM1/XIAP
## GO:0016032 GO:0016032         viral process     1       1/3            CDK1
## GO:0022414 GO:0022414  reproductive process     1       1/3            CDK1
##                    ID                Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex     2       2/3
## GO:0044423 GO:0044423           virion component     0       0/3
## GO:0110165 GO:0110165 cellular anatomical entity     3       3/3
##                     geneID
## GO:0032991      CDK1/FOXM1
## GO:0044423                
## GO:0110165 CDK1/FOXM1/XIAP
##                    ID                  Description Count GeneRatio
## GO:0003774 GO:0003774  cytoskeletal motor activity     0       0/4
## GO:0003824 GO:0003824           catalytic activity     2       2/4
## GO:0005198 GO:0005198 structural molecule activity     0       0/4
## GO:0005215 GO:0005215         transporter activity     0       0/4
## GO:0005488 GO:0005488                      binding     4       4/4
## GO:0009055 GO:0009055   electron transfer activity     0       0/4
##                           geneID
## GO:0003774                      
## GO:0003824            MAPK3/XIAP
## GO:0005198                      
## GO:0005215                      
## GO:0005488 MAPK3/FOXM1/XIAP/TFRC
## GO:0009055                      
##                    ID           Description Count GeneRatio
## GO:0000003 GO:0000003          reproduction     0       0/4
## GO:0002376 GO:0002376 immune system process     3       3/4
## GO:0008152 GO:0008152     metabolic process     4       4/4
## GO:0009987 GO:0009987      cellular process     4       4/4
## GO:0016032 GO:0016032         viral process     1       1/4
## GO:0022414 GO:0022414  reproductive process     0       0/4
##                           geneID
## GO:0000003                      
## GO:0002376       MAPK3/XIAP/TFRC
## GO:0008152 MAPK3/FOXM1/XIAP/TFRC
## GO:0009987 MAPK3/FOXM1/XIAP/TFRC
## GO:0016032                  TFRC
## GO:0022414                      
##                    ID                Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex     2       2/4
## GO:0044423 GO:0044423           virion component     0       0/4
## GO:0110165 GO:0110165 cellular anatomical entity     4       4/4
##                           geneID
## GO:0032991            FOXM1/TFRC
## GO:0044423                      
## GO:0110165 MAPK3/FOXM1/XIAP/TFRC
##                    ID                  Description Count GeneRatio
## GO:0003774 GO:0003774  cytoskeletal motor activity     0      0/12
## GO:0003824 GO:0003824           catalytic activity     6      6/12
## GO:0005198 GO:0005198 structural molecule activity     1      1/12
## GO:0005215 GO:0005215         transporter activity     0      0/12
## GO:0005488 GO:0005488                      binding    12     12/12
## GO:0009055 GO:0009055   electron transfer activity     0      0/12
##                                                                       geneID
## GO:0003774                                                                  
## GO:0003824                                    PRKCD/AKT1/MAPK3/TYMS/XIAP/RET
## GO:0005198                                                             CLDN7
## GO:0005215                                                                  
## GO:0005488 PRKCD/AKT1/MAPK3/WWTR1/TYMS/FOXM1/XIAP/PREX1/RET/TFRC/CLDN7/ANXA1
## GO:0009055                                                                  
##                    ID           Description Count GeneRatio
## GO:0000003 GO:0000003          reproduction     1      1/12
## GO:0002376 GO:0002376 immune system process     8      8/12
## GO:0008152 GO:0008152     metabolic process    11     11/12
## GO:0009987 GO:0009987      cellular process    12     12/12
## GO:0016032 GO:0016032         viral process     2      2/12
## GO:0022414 GO:0022414  reproductive process     1      1/12
##                                                                       geneID
## GO:0000003                                                              AKT1
## GO:0002376                        PRKCD/AKT1/MAPK3/XIAP/PREX1/RET/TFRC/ANXA1
## GO:0008152       PRKCD/AKT1/MAPK3/WWTR1/TYMS/FOXM1/XIAP/PREX1/RET/TFRC/ANXA1
## GO:0009987 PRKCD/AKT1/MAPK3/WWTR1/TYMS/FOXM1/XIAP/PREX1/RET/TFRC/CLDN7/ANXA1
## GO:0016032                                                         AKT1/TFRC
## GO:0022414                                                              AKT1
##                    ID                Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex     5      5/12
## GO:0044423 GO:0044423           virion component     0      0/12
## GO:0110165 GO:0110165 cellular anatomical entity    12     12/12
##                                                                       geneID
## GO:0032991                                         AKT1/WWTR1/FOXM1/RET/TFRC
## GO:0044423                                                                  
## GO:0110165 PRKCD/AKT1/MAPK3/WWTR1/TYMS/FOXM1/XIAP/PREX1/RET/TFRC/CLDN7/ANXA1
##                    ID                  Description Count GeneRatio
## GO:0003774 GO:0003774  cytoskeletal motor activity     0      0/12
## GO:0003824 GO:0003824           catalytic activity     8      8/12
## GO:0005198 GO:0005198 structural molecule activity     0      0/12
## GO:0005215 GO:0005215         transporter activity     0      0/12
## GO:0005488 GO:0005488                      binding    12     12/12
## GO:0009055 GO:0009055   electron transfer activity     0      0/12
##                                                                         geneID
## GO:0003774                                                                    
## GO:0003824                        RAD51/MAPK9/MAPK3/CHEK1/CDK1/EEF2K/TYMS/XIAP
## GO:0005198                                                                    
## GO:0005215                                                                    
## GO:0005488 RAD51/MAPK9/MAPK3/CHEK1/CDK1/EEF2K/TYMS/FOXM1/XIAP/PREX1/TFRC/ANXA1
## GO:0009055                                                                    
##                    ID           Description Count GeneRatio
## GO:0000003 GO:0000003          reproduction     2      2/12
## GO:0002376 GO:0002376 immune system process     6      6/12
## GO:0008152 GO:0008152     metabolic process    12     12/12
## GO:0009987 GO:0009987      cellular process    12     12/12
## GO:0016032 GO:0016032         viral process     2      2/12
## GO:0022414 GO:0022414  reproductive process     2      2/12
##                                                                         geneID
## GO:0000003                                                          RAD51/CDK1
## GO:0002376                                   MAPK9/MAPK3/XIAP/PREX1/TFRC/ANXA1
## GO:0008152 RAD51/MAPK9/MAPK3/CHEK1/CDK1/EEF2K/TYMS/FOXM1/XIAP/PREX1/TFRC/ANXA1
## GO:0009987 RAD51/MAPK9/MAPK3/CHEK1/CDK1/EEF2K/TYMS/FOXM1/XIAP/PREX1/TFRC/ANXA1
## GO:0016032                                                           CDK1/TFRC
## GO:0022414                                                          RAD51/CDK1
##                    ID                Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex     5      5/12
## GO:0044423 GO:0044423           virion component     0      0/12
## GO:0110165 GO:0110165 cellular anatomical entity    12     12/12
##                                                                         geneID
## GO:0032991                                         RAD51/CHEK1/CDK1/FOXM1/TFRC
## GO:0044423                                                                    
## GO:0110165 RAD51/MAPK9/MAPK3/CHEK1/CDK1/EEF2K/TYMS/FOXM1/XIAP/PREX1/TFRC/ANXA1
##                    ID                  Description Count GeneRatio
## GO:0003774 GO:0003774  cytoskeletal motor activity     0      0/13
## GO:0003824 GO:0003824           catalytic activity     8      8/13
## GO:0005198 GO:0005198 structural molecule activity     0      0/13
## GO:0005215 GO:0005215         transporter activity     0      0/13
## GO:0005488 GO:0005488                      binding    13     13/13
## GO:0009055 GO:0009055   electron transfer activity     0      0/13
##                                                                               geneID
## GO:0003774                                                                          
## GO:0003824                              RAD51/MAPK9/MAPK3/CHEK1/CDK1/EEF2K/TYMS/XIAP
## GO:0005198                                                                          
## GO:0005215                                                                          
## GO:0005488 RAD51/MAPK9/MAPK3/STMN1/CHEK1/CDK1/EEF2K/TYMS/FOXM1/XIAP/PREX1/TFRC/ANXA1
## GO:0009055                                                                          
##                    ID           Description Count GeneRatio
## GO:0000003 GO:0000003          reproduction     2      2/13
## GO:0002376 GO:0002376 immune system process     6      6/13
## GO:0008152 GO:0008152     metabolic process    12     12/13
## GO:0009987 GO:0009987      cellular process    13     13/13
## GO:0016032 GO:0016032         viral process     2      2/13
## GO:0022414 GO:0022414  reproductive process     2      2/13
##                                                                               geneID
## GO:0000003                                                                RAD51/CDK1
## GO:0002376                                         MAPK9/MAPK3/XIAP/PREX1/TFRC/ANXA1
## GO:0008152       RAD51/MAPK9/MAPK3/CHEK1/CDK1/EEF2K/TYMS/FOXM1/XIAP/PREX1/TFRC/ANXA1
## GO:0009987 RAD51/MAPK9/MAPK3/STMN1/CHEK1/CDK1/EEF2K/TYMS/FOXM1/XIAP/PREX1/TFRC/ANXA1
## GO:0016032                                                                 CDK1/TFRC
## GO:0022414                                                                RAD51/CDK1
##                    ID                Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex     5      5/13
## GO:0044423 GO:0044423           virion component     0      0/13
## GO:0110165 GO:0110165 cellular anatomical entity    13     13/13
##                                                                               geneID
## GO:0032991                                               RAD51/CHEK1/CDK1/FOXM1/TFRC
## GO:0044423                                                                          
## GO:0110165 RAD51/MAPK9/MAPK3/STMN1/CHEK1/CDK1/EEF2K/TYMS/FOXM1/XIAP/PREX1/TFRC/ANXA1
##                    ID                  Description Count GeneRatio
## GO:0003774 GO:0003774  cytoskeletal motor activity     0       0/4
## GO:0003824 GO:0003824           catalytic activity     2       2/4
## GO:0005198 GO:0005198 structural molecule activity     0       0/4
## GO:0005215 GO:0005215         transporter activity     0       0/4
## GO:0005488 GO:0005488                      binding     4       4/4
## GO:0009055 GO:0009055   electron transfer activity     0       0/4
##                           geneID
## GO:0003774                      
## GO:0003824            MAPK3/XIAP
## GO:0005198                      
## GO:0005215                      
## GO:0005488 MAPK3/FOXM1/XIAP/TFRC
## GO:0009055                      
##                    ID           Description Count GeneRatio
## GO:0000003 GO:0000003          reproduction     0       0/4
## GO:0002376 GO:0002376 immune system process     3       3/4
## GO:0008152 GO:0008152     metabolic process     4       4/4
## GO:0009987 GO:0009987      cellular process     4       4/4
## GO:0016032 GO:0016032         viral process     1       1/4
## GO:0022414 GO:0022414  reproductive process     0       0/4
##                           geneID
## GO:0000003                      
## GO:0002376       MAPK3/XIAP/TFRC
## GO:0008152 MAPK3/FOXM1/XIAP/TFRC
## GO:0009987 MAPK3/FOXM1/XIAP/TFRC
## GO:0016032                  TFRC
## GO:0022414                      
##                    ID                Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex     2       2/4
## GO:0044423 GO:0044423           virion component     0       0/4
## GO:0110165 GO:0110165 cellular anatomical entity     4       4/4
##                           geneID
## GO:0032991            FOXM1/TFRC
## GO:0044423                      
## GO:0110165 MAPK3/FOXM1/XIAP/TFRC
##                    ID                  Description Count GeneRatio geneID
## GO:0003774 GO:0003774  cytoskeletal motor activity     0       0/1       
## GO:0003824 GO:0003824           catalytic activity     0       0/1       
## GO:0005198 GO:0005198 structural molecule activity     0       0/1       
## GO:0005215 GO:0005215         transporter activity     0       0/1       
## GO:0005488 GO:0005488                      binding     1       1/1  FOXM1
## GO:0009055 GO:0009055   electron transfer activity     0       0/1       
##                    ID           Description Count GeneRatio geneID
## GO:0000003 GO:0000003          reproduction     0       0/1       
## GO:0002376 GO:0002376 immune system process     0       0/1       
## GO:0008152 GO:0008152     metabolic process     1       1/1  FOXM1
## GO:0009987 GO:0009987      cellular process     1       1/1  FOXM1
## GO:0016032 GO:0016032         viral process     0       0/1       
## GO:0022414 GO:0022414  reproductive process     0       0/1       
##                    ID                Description Count GeneRatio geneID
## GO:0032991 GO:0032991 protein-containing complex     1       1/1  FOXM1
## GO:0044423 GO:0044423           virion component     0       0/1       
## GO:0110165 GO:0110165 cellular anatomical entity     1       1/1  FOXM1
barplot(ggo_MF[[1]], title = "groupGO, Molecular Function, \n 3-Fold CV, alpha = 0.5, Deviance")

barplot(ggo_MF[[2]], title = "groupGO, Molecular Function, \n 3-Fold CV, alpha = 0.5, C-Index")

barplot(ggo_MF[[3]], title = "groupGO, Molecular Function, \n 3-Fold CV, alpha = 1, Deviance")

barplot(ggo_MF[[4]], title = "groupGO, Molecular Function, \n 3-Fold CV, alpha = 1, C-Index")

#barplot(ggo_MF[[5]], title = "groupGO, Molecular Function, \n 5-Fold CV, alpha = 0.5, Deviance")
barplot(ggo_MF[[5]], title = "groupGO, Molecular Function, \n 5-Fold CV, alpha = 0.5, C-Index")

barplot(ggo_MF[[6]], title = "groupGO, Molecular Function, \n 5-Fold CV, alpha = 1, Deviance")

barplot(ggo_MF[[7]], title = "groupGO, Molecular Function, \n 5-Fold CV, alpha = 1, C-Index")

barplot(ggo_MF[[8]], title = "groupGO, Molecular Function, \n 10-Fold CV, alpha = 0.5, Deviance")

barplot(ggo_MF[[9]], title = "groupGO, Molecular Function, \n 10-Fold CV, alpha = 0.5, C-Index")

barplot(ggo_MF[[10]], title = "groupGO, Molecular Function, \n 10-Fold CV, alpha = 1, Deviance")

barplot(ggo_MF[[11]], title = "groupGO, Molecular Function, \n 10-Fold CV, alpha = 1, C-Index")

barplot(ggo_BP[[1]], title = "groupGO, Biological Process, \n 3-Fold CV, alpha = 0.5, Deviance")

barplot(ggo_BP[[2]], title = "groupGO, Biological Process, \n 3-Fold CV, alpha = 0.5, C-Index")

barplot(ggo_BP[[3]], title = "groupGO, Biological Process, \n 3-Fold CV, alpha = 1, Deviance")

barplot(ggo_BP[[4]], title = "groupGO, Biological Process, \n 3-Fold CV, alpha = 1, C-Index")

#barplot(ggo_BP[[5]], title = "groupGO, Biological Process, \n 5-Fold CV, alpha = 0.5, Deviance")
barplot(ggo_BP[[5]], title = "groupGO, Biological Process, \n 5-Fold CV, alpha = 0.5, C-Index")

barplot(ggo_BP[[6]], title = "groupGO, Biological Process, \n 5-Fold CV, alpha = 1, Deviance")

barplot(ggo_BP[[7]], title = "groupGO, Biological Process, \n 5-Fold CV, alpha = 1, C-Index")

barplot(ggo_BP[[8]], title = "groupGO, Biological Process, \n 10-Fold CV, alpha = 0.5, Deviance")

barplot(ggo_BP[[9]], title = "groupGO, Biological Process, \n 10-Fold CV, alpha = 0.5, C-Index")

barplot(ggo_BP[[10]], title = "groupGO, Biological Process, \n 10-Fold CV, alpha = 1, Deviance")

barplot(ggo_BP[[11]], title = "groupGO, Biological Process, \n 10-Fold CV, alpha = 1, C-Index")

barplot(ggo_CC[[1]], title = "groupGO, Cellular Component, \n 3-Fold CV, alpha = 0.5, Deviance")

barplot(ggo_CC[[2]], title = "groupGO, Cellular Component, \n 3-Fold CV, alpha = 0.5, C-Index")

barplot(ggo_CC[[3]], title = "groupGO, Cellular Component, \n 3-Fold CV, alpha = 1, Deviance")

barplot(ggo_CC[[4]], title = "groupGO, Cellular Component, \n 3-Fold CV, alpha = 1, C-Index")

#barplot(ggo_CC[[5]], title = "groupGO, Cellular Component, \n 5-Fold CV, alpha = 0.5, Deviance")
barplot(ggo_CC[[5]], title = "groupGO, Cellular Component, \n 5-Fold CV, alpha = 0.5, C-Index")

barplot(ggo_CC[[6]], title = "groupGO, Cellular Component, \n 5-Fold CV, alpha = 1, Deviance")

barplot(ggo_CC[[7]], title = "groupGO, Cellular Component, \n 5-Fold CV, alpha = 1, C-Index")

barplot(ggo_CC[[8]], title = "groupGO, Cellular Component, \n 10-Fold CV, alpha = 0.5, Deviance")

barplot(ggo_CC[[9]], title = "groupGO, Cellular Component, \n 10-Fold CV, alpha = 0.5, C-Index")

barplot(ggo_CC[[10]], title = "groupGO, Cellular Component, \n 10-Fold CV, alpha = 1, Deviance")

barplot(ggo_CC[[11]], title = "groupGO, Cellular Component, \n 10-Fold CV, alpha = 1, C-Index")

B. GO Over-Representation

ego_MF <- list()#GO enrichment of a geneset for Molecular Function
ego_BP <- list()#GO enrichment of a geneset for Biological Process
ego_CC <- list()#GO enrichment of a geneset for Cellular Component


for(z in 1:length(geneNames)){
  print(z)
  input <- geneNames[[z]]
  ego_MF[[z]] <- enrichGO(
    gene          = input,
    OrgDb         = org.Hs.eg.db,
    ont           = "MF",
    pAdjustMethod = "BH",
    keyType="SYMBOL",
    pvalueCutoff  = 0.05,
    qvalueCutoff  = 0.05,
    minGSSize     = 2,
    readable      = TRUE)
  
  ego_BP[[z]] <- enrichGO(
    gene          = input,
    OrgDb         = org.Hs.eg.db,
    ont           = "BP",
    pAdjustMethod = "BH",
    keyType="SYMBOL",
    pvalueCutoff  = 0.05,
    qvalueCutoff  = 0.05,
    minGSSize     = 2,
    readable      = TRUE)
  
  ego_CC[[z]] <- enrichGO(
    gene          = input,
    OrgDb         = org.Hs.eg.db,
    ont           = "CC",
    pAdjustMethod = "BH",
    keyType="SYMBOL",
    pvalueCutoff  = 0.05,
    qvalueCutoff  = 0.05,
    minGSSize     = 2,
    readable      = TRUE)
}
## [1] 1
## [1] 2
## [1] 3
## [1] 4
## [1] 5
## [1] 6
## [1] 7
## [1] 8
## [1] 9
## [1] 10
## [1] 11
## No gene sets have size between 2 and 500 ...
## --> return NULL...
## No gene sets have size between 2 and 500 ...
## --> return NULL...
for(z in 1:(length(geneNames)-1)){ #11th element is null
  print(head(ego_MF[[z]]))
  print(head(ego_BP[[z]]))
  print(head(ego_CC[[z]]))
}
##                    ID                                       Description
## GO:0004674 GO:0004674          protein serine/threonine kinase activity
## GO:0106310 GO:0106310                    protein serine kinase activity
## GO:0004707 GO:0004707                               MAP kinase activity
## GO:0035173 GO:0035173                           histone kinase activity
## GO:0004712 GO:0004712 protein serine/threonine/tyrosine kinase activity
## GO:0030544 GO:0030544                             Hsp70 protein binding
##            GeneRatio   BgRatio       pvalue     p.adjust       qvalue
## GO:0004674      6/16 427/18522 9.542515e-07 0.0001011507 4.921929e-05
## GO:0106310      5/16 363/18522 1.028418e-05 0.0005450614 2.652235e-04
## GO:0004707      2/16  16/18522 8.336346e-05 0.0029455088 1.433266e-03
## GO:0035173      2/16  23/18522 1.751391e-04 0.0046411863 2.258373e-03
## GO:0004712      2/16  43/18522 6.188351e-04 0.0131193047 6.383773e-03
## GO:0030544      2/16  51/18522 8.702575e-04 0.0153745500 7.481161e-03
##                                       geneID Count
## GO:0004674 AKT1/MAPK9/MAPK3/CHEK1/CDK1/EEF2K     6
## GO:0106310       AKT1/MAPK9/MAPK3/CHEK1/CDK1     5
## GO:0004707                       MAPK9/MAPK3     2
## GO:0035173                        CHEK1/CDK1     2
## GO:0004712                        AKT1/MAPK9     2
## GO:0030544                         CDK1/TFRC     2
##                    ID                                   Description GeneRatio
## GO:0051054 GO:0051054  positive regulation of DNA metabolic process      6/16
## GO:0046686 GO:0046686                       response to cadmium ion      4/16
## GO:0010038 GO:0010038                         response to metal ion      6/16
## GO:0042770 GO:0042770 signal transduction in response to DNA damage      5/16
## GO:0071241 GO:0071241      cellular response to inorganic substance      5/16
## GO:0097305 GO:0097305                           response to alcohol      5/16
##              BgRatio       pvalue     p.adjust       qvalue
## GO:0051054 301/18888 1.091160e-07 0.0001151941 5.086625e-05
## GO:0046686  60/18888 1.627035e-07 0.0001151941 5.086625e-05
## GO:0010038 360/18888 3.134135e-07 0.0001310348 5.786105e-05
## GO:0042770 188/18888 3.701549e-07 0.0001310348 5.786105e-05
## GO:0071241 229/18888 9.823528e-07 0.0002782023 1.228458e-04
## GO:0097305 259/18888 1.800691e-06 0.0004249632 1.876510e-04
##                                      geneID Count
## GO:0051054 AKT1/RAD51/MAPK3/CDK1/FOXM1/TFRC     6
## GO:0046686            AKT1/MAPK9/MAPK3/CDK1     4
## GO:0010038 AKT1/MAPK9/MAPK3/CDK1/EEF2K/TFRC     6
## GO:0042770     RAD51/MAPK3/CHEK1/CDK1/FOXM1     5
## GO:0071241     AKT1/RAD51/MAPK9/MAPK3/EEF2K     5
## GO:0097305       AKT1/RAD51/CDK1/TYMS/CLDN7     5
##                    ID                  Description GeneRatio   BgRatio
## GO:0005769 GO:0005769               early endosome      4/16 428/19894
## GO:0000781 GO:0000781 chromosome, telomeric region      3/16 173/19894
## GO:0016323 GO:0016323  basolateral plasma membrane      3/16 255/19894
## GO:0016328 GO:0016328      lateral plasma membrane      2/16  68/19894
## GO:0009925 GO:0009925        basal plasma membrane      3/16 286/19894
## GO:0097122 GO:0097122       cyclin A2-CDK1 complex      1/16   2/19894
##                  pvalue   p.adjust     qvalue               geneID Count
## GO:0005769 0.0003131011 0.01598376 0.01139194 MAPK3/RET/TFRC/ANXA1     4
## GO:0000781 0.0003329950 0.01598376 0.01139194     RAD51/CHEK1/CDK1     3
## GO:0016323 0.0010300925 0.01817677 0.01295494     TFRC/CLDN7/ANXA1     3
## GO:0016328 0.0013393677 0.01817677 0.01295494          CLDN7/ANXA1     2
## GO:0009925 0.0014331728 0.01817677 0.01295494     TFRC/CLDN7/ANXA1     3
## GO:0097122 0.0016079187 0.01817677 0.01295494                 CDK1     1
##                    ID                              Description GeneRatio
## GO:0004674 GO:0004674 protein serine/threonine kinase activity      5/12
## GO:0004707 GO:0004707                      MAP kinase activity      2/12
## GO:0106310 GO:0106310           protein serine kinase activity      4/12
## GO:0035173 GO:0035173                  histone kinase activity      2/12
## GO:0030544 GO:0030544                    Hsp70 protein binding      2/12
## GO:0001618 GO:0001618                  virus receptor activity      2/12
##              BgRatio       pvalue     p.adjust       qvalue
## GO:0004674 427/18522 4.408109e-06 0.0003702811 0.0001484837
## GO:0004707  16/18522 4.594242e-05 0.0017757774 0.0007120912
## GO:0106310 363/18522 6.342062e-05 0.0017757774 0.0007120912
## GO:0035173  23/18522 9.661815e-05 0.0020289811 0.0008136265
## GO:0030544  51/18522 4.820265e-04 0.0080980457 0.0032473366
## GO:0001618  79/18522 1.153123e-03 0.0108811215 0.0043633570
##                                  geneID Count
## GO:0004674 MAPK9/MAPK3/CHEK1/CDK1/EEF2K     5
## GO:0004707                  MAPK9/MAPK3     2
## GO:0106310       MAPK9/MAPK3/CHEK1/CDK1     4
## GO:0035173                   CHEK1/CDK1     2
## GO:0030544                    CDK1/TFRC     2
## GO:0001618                    CDK1/TFRC     2
##                    ID                                   Description GeneRatio
## GO:0042770 GO:0042770 signal transduction in response to DNA damage      5/12
## GO:0051054 GO:0051054  positive regulation of DNA metabolic process      5/12
## GO:0010038 GO:0010038                         response to metal ion      5/12
## GO:0046686 GO:0046686                       response to cadmium ion      3/12
## GO:0071241 GO:0071241      cellular response to inorganic substance      4/12
## GO:0048308 GO:0048308                         organelle inheritance      2/12
##              BgRatio       pvalue     p.adjust       qvalue
## GO:0042770 188/18888 6.932499e-08 6.544279e-05 2.875163e-05
## GO:0051054 301/18888 7.184948e-07 3.391296e-04 1.489931e-04
## GO:0010038 360/18888 1.735716e-06 5.461720e-04 2.399551e-04
## GO:0046686  60/18888 6.569175e-06 1.550325e-03 6.811197e-04
## GO:0071241 229/18888 9.653169e-06 1.822518e-03 8.007049e-04
## GO:0048308  15/18888 3.867417e-05 5.215488e-03 2.291372e-03
##                                  geneID Count
## GO:0042770 RAD51/MAPK3/CHEK1/CDK1/FOXM1     5
## GO:0051054  RAD51/MAPK3/CDK1/FOXM1/TFRC     5
## GO:0010038  MAPK9/MAPK3/CDK1/EEF2K/TFRC     5
## GO:0046686             MAPK9/MAPK3/CDK1     3
## GO:0071241      RAD51/MAPK9/MAPK3/EEF2K     4
## GO:0048308                   MAPK3/CDK1     2
##                    ID                                    Description GeneRatio
## GO:0000781 GO:0000781                   chromosome, telomeric region      3/12
## GO:0000794 GO:0000794                   condensed nuclear chromosome      2/12
## GO:0097122 GO:0097122                         cyclin A2-CDK1 complex      1/12
## GO:0097125 GO:0097125                         cyclin B1-CDK1 complex      1/12
## GO:0099182 GO:0099182 presynaptic intermediate filament cytoskeleton      1/12
## GO:0098687 GO:0098687                             chromosomal region      3/12
##              BgRatio       pvalue   p.adjust      qvalue           geneID Count
## GO:0000781 173/19894 0.0001342138 0.01167660 0.007346439 RAD51/CHEK1/CDK1     3
## GO:0000794  81/19894 0.0010524418 0.02098545 0.013203187      RAD51/CHEK1     2
## GO:0097122   2/19894 0.0012060603 0.02098545 0.013203187             CDK1     1
## GO:0097125   2/19894 0.0012060603 0.02098545 0.013203187             CDK1     1
## GO:0099182   2/19894 0.0012060603 0.02098545 0.013203187            RAD51     1
## GO:0098687 402/19894 0.0015730314 0.02280896 0.014350462 RAD51/CHEK1/CDK1     3
##                    ID
## GO:0004998 GO:0004998
## GO:0120283 GO:0120283
## GO:0004707 GO:0004707
## GO:0043027 GO:0043027
## GO:0004869 GO:0004869
## GO:0043028 GO:0043028
##                                                                             Description
## GO:0004998                                                transferrin receptor activity
## GO:0120283                                      protein serine/threonine kinase binding
## GO:0004707                                                          MAP kinase activity
## GO:0043027 cysteine-type endopeptidase inhibitor activity involved in apoptotic process
## GO:0004869                               cysteine-type endopeptidase inhibitor activity
## GO:0043028 cysteine-type endopeptidase regulator activity involved in apoptotic process
##            GeneRatio  BgRatio       pvalue   p.adjust      qvalue geneID Count
## GO:0004998       1/4  2/18522 0.0004318838 0.01295651 0.004091531   TFRC     1
## GO:0120283       1/4  7/18522 0.0015109813 0.02266472 0.007157280   XIAP     1
## GO:0004707       1/4 16/18522 0.0034511548 0.03234409 0.010213925  MAPK3     1
## GO:0043027       1/4 20/18522 0.0043125460 0.03234409 0.010213925   XIAP     1
## GO:0004869       1/4 37/18522 0.0079672300 0.03961505 0.012510017   XIAP     1
## GO:0043028       1/4 42/18522 0.0090402197 0.03961505 0.012510017   XIAP     1
##                    ID
## GO:0051054 GO:0051054
## GO:0032872 GO:0032872
## GO:0070302 GO:0070302
## GO:0051403 GO:0051403
## GO:0031098 GO:0031098
## GO:1902528 GO:1902528
##                                                                Description
## GO:0051054                    positive regulation of DNA metabolic process
## GO:0032872                     regulation of stress-activated MAPK cascade
## GO:0070302 regulation of stress-activated protein kinase signaling cascade
## GO:0051403                                   stress-activated MAPK cascade
## GO:0031098               stress-activated protein kinase signaling cascade
## GO:1902528                 regulation of protein linear polyubiquitination
##            GeneRatio   BgRatio       pvalue    p.adjust       qvalue
## GO:0051054       3/4 301/18888 1.584016e-05 0.003341572 0.0009517791
## GO:0032872       2/4  35/18888 1.996811e-05 0.003341572 0.0009517791
## GO:0070302       2/4  38/18888 2.358757e-05 0.003341572 0.0009517791
## GO:0051403       2/4  50/18888 4.106724e-05 0.004363395 0.0012428244
## GO:0031098       2/4  59/18888 5.732355e-05 0.004872502 0.0013878333
## GO:1902528       1/4   2/18888 4.235157e-04 0.020667597 0.0058867459
##                      geneID Count
## GO:0051054 MAPK3/FOXM1/TFRC     3
## GO:0032872      MAPK3/FOXM1     2
## GO:0070302      MAPK3/FOXM1     2
## GO:0051403      MAPK3/FOXM1     2
## GO:0031098      MAPK3/FOXM1     2
## GO:1902528             XIAP     1
##                    ID                      Description GeneRatio   BgRatio
## GO:1990712 GO:1990712 HFE-transferrin receptor complex       1/4   8/19894
## GO:0005769 GO:0005769                   early endosome       2/4 428/19894
## GO:0031143 GO:0031143                     pseudopodium       1/4  18/19894
##                 pvalue   p.adjust     qvalue     geneID Count
## GO:1990712 0.001607676 0.03855515 0.01902392       TFRC     1
## GO:0005769 0.002692287 0.03855515 0.01902392 MAPK3/TFRC     2
## GO:0031143 0.003614545 0.03855515 0.01902392      MAPK3     1
##                    ID
## GO:0004998 GO:0004998
## GO:0120283 GO:0120283
## GO:0004707 GO:0004707
## GO:0043027 GO:0043027
## GO:0004869 GO:0004869
## GO:0043028 GO:0043028
##                                                                             Description
## GO:0004998                                                transferrin receptor activity
## GO:0120283                                      protein serine/threonine kinase binding
## GO:0004707                                                          MAP kinase activity
## GO:0043027 cysteine-type endopeptidase inhibitor activity involved in apoptotic process
## GO:0004869                               cysteine-type endopeptidase inhibitor activity
## GO:0043028 cysteine-type endopeptidase regulator activity involved in apoptotic process
##            GeneRatio  BgRatio       pvalue   p.adjust      qvalue geneID Count
## GO:0004998       1/4  2/18522 0.0004318838 0.01295651 0.004091531   TFRC     1
## GO:0120283       1/4  7/18522 0.0015109813 0.02266472 0.007157280   XIAP     1
## GO:0004707       1/4 16/18522 0.0034511548 0.03234409 0.010213925  MAPK3     1
## GO:0043027       1/4 20/18522 0.0043125460 0.03234409 0.010213925   XIAP     1
## GO:0004869       1/4 37/18522 0.0079672300 0.03961505 0.012510017   XIAP     1
## GO:0043028       1/4 42/18522 0.0090402197 0.03961505 0.012510017   XIAP     1
##                    ID
## GO:0051054 GO:0051054
## GO:0032872 GO:0032872
## GO:0070302 GO:0070302
## GO:0051403 GO:0051403
## GO:0031098 GO:0031098
## GO:1902528 GO:1902528
##                                                                Description
## GO:0051054                    positive regulation of DNA metabolic process
## GO:0032872                     regulation of stress-activated MAPK cascade
## GO:0070302 regulation of stress-activated protein kinase signaling cascade
## GO:0051403                                   stress-activated MAPK cascade
## GO:0031098               stress-activated protein kinase signaling cascade
## GO:1902528                 regulation of protein linear polyubiquitination
##            GeneRatio   BgRatio       pvalue    p.adjust       qvalue
## GO:0051054       3/4 301/18888 1.584016e-05 0.003341572 0.0009517791
## GO:0032872       2/4  35/18888 1.996811e-05 0.003341572 0.0009517791
## GO:0070302       2/4  38/18888 2.358757e-05 0.003341572 0.0009517791
## GO:0051403       2/4  50/18888 4.106724e-05 0.004363395 0.0012428244
## GO:0031098       2/4  59/18888 5.732355e-05 0.004872502 0.0013878333
## GO:1902528       1/4   2/18888 4.235157e-04 0.020667597 0.0058867459
##                      geneID Count
## GO:0051054 MAPK3/FOXM1/TFRC     3
## GO:0032872      MAPK3/FOXM1     2
## GO:0070302      MAPK3/FOXM1     2
## GO:0051403      MAPK3/FOXM1     2
## GO:0031098      MAPK3/FOXM1     2
## GO:1902528             XIAP     1
##                    ID                      Description GeneRatio   BgRatio
## GO:1990712 GO:1990712 HFE-transferrin receptor complex       1/4   8/19894
## GO:0005769 GO:0005769                   early endosome       2/4 428/19894
## GO:0031143 GO:0031143                     pseudopodium       1/4  18/19894
##                 pvalue   p.adjust     qvalue     geneID Count
## GO:1990712 0.001607676 0.03855515 0.01902392       TFRC     1
## GO:0005769 0.002692287 0.03855515 0.01902392 MAPK3/TFRC     2
## GO:0031143 0.003614545 0.03855515 0.01902392      MAPK3     1
##                    ID
## GO:0120283 GO:0120283
## GO:0008353 GO:0008353
## GO:0043027 GO:0043027
## GO:0035173 GO:0035173
## GO:0140994 GO:0140994
## GO:0004693 GO:0004693
##                                                                             Description
## GO:0120283                                      protein serine/threonine kinase binding
## GO:0008353                    RNA polymerase II CTD heptapeptide repeat kinase activity
## GO:0043027 cysteine-type endopeptidase inhibitor activity involved in apoptotic process
## GO:0035173                                                      histone kinase activity
## GO:0140994                 RNA polymerase II CTD heptapeptide repeat modifying activity
## GO:0004693                    cyclin-dependent protein serine/threonine kinase activity
##            GeneRatio  BgRatio      pvalue   p.adjust      qvalue geneID Count
## GO:0120283       1/3  7/18522 0.001133420 0.01860828 0.005596474   XIAP     1
## GO:0008353       1/3 10/18522 0.001618909 0.01860828 0.005596474   CDK1     1
## GO:0043027       1/3 20/18522 0.003236069 0.01860828 0.005596474   XIAP     1
## GO:0035173       1/3 23/18522 0.003720876 0.01860828 0.005596474   CDK1     1
## GO:0140994       1/3 23/18522 0.003720876 0.01860828 0.005596474   CDK1     1
## GO:0004693       1/3 29/18522 0.004690019 0.01860828 0.005596474   CDK1     1
##                    ID                                              Description
## GO:0000086 GO:0000086                    G2/M transition of mitotic cell cycle
## GO:0044839 GO:0044839                         cell cycle G2/M phase transition
## GO:0042770 GO:0042770            signal transduction in response to DNA damage
## GO:1902528 GO:1902528          regulation of protein linear polyubiquitination
## GO:1902530 GO:1902530 positive regulation of protein linear polyubiquitination
## GO:0014038 GO:0014038               regulation of Schwann cell differentiation
##            GeneRatio   BgRatio       pvalue   p.adjust      qvalue     geneID
## GO:0000086       2/3 136/18888 0.0001536688 0.01772460 0.002808652 CDK1/FOXM1
## GO:0044839       2/3 152/18888 0.0001919938 0.01772460 0.002808652 CDK1/FOXM1
## GO:0042770       2/3 188/18888 0.0002937047 0.01772460 0.002808652 CDK1/FOXM1
## GO:1902528       1/3   2/18888 0.0003176452 0.01772460 0.002808652       XIAP
## GO:1902530       1/3   2/18888 0.0003176452 0.01772460 0.002808652       XIAP
## GO:0014038       1/3   4/18888 0.0006352231 0.02084585 0.003303247       CDK1
##            Count
## GO:0000086     2
## GO:0044839     2
## GO:0042770     2
## GO:1902528     1
## GO:1902530     1
## GO:0014038     1
##                    ID                                        Description
## GO:0097122 GO:0097122                             cyclin A2-CDK1 complex
## GO:0097125 GO:0097125                             cyclin B1-CDK1 complex
## GO:0000307 GO:0000307 cyclin-dependent protein kinase holoenzyme complex
## GO:0005876 GO:0005876                                spindle microtubule
## GO:1902554 GO:1902554            serine/threonine protein kinase complex
## GO:1902911 GO:1902911                             protein kinase complex
##            GeneRatio   BgRatio       pvalue    p.adjust       qvalue geneID
## GO:0097122       1/3   2/19894 0.0003015833 0.002111083 0.0006349122   CDK1
## GO:0097125       1/3   2/19894 0.0003015833 0.002111083 0.0006349122   CDK1
## GO:0000307       1/3  56/19894 0.0084214303 0.039300008 0.0118195514   CDK1
## GO:0005876       1/3  82/19894 0.0123152550 0.043103393 0.0129634264   CDK1
## GO:1902554       1/3 136/19894 0.0203698303 0.047596740 0.0143148091   CDK1
## GO:1902911       1/3 150/19894 0.0224508810 0.047596740 0.0143148091   CDK1
##            Count
## GO:0097122     1
## GO:0097125     1
## GO:0000307     1
## GO:0005876     1
## GO:1902554     1
## GO:1902911     1
##                    ID
## GO:0004998 GO:0004998
## GO:0120283 GO:0120283
## GO:0004707 GO:0004707
## GO:0043027 GO:0043027
## GO:0004869 GO:0004869
## GO:0043028 GO:0043028
##                                                                             Description
## GO:0004998                                                transferrin receptor activity
## GO:0120283                                      protein serine/threonine kinase binding
## GO:0004707                                                          MAP kinase activity
## GO:0043027 cysteine-type endopeptidase inhibitor activity involved in apoptotic process
## GO:0004869                               cysteine-type endopeptidase inhibitor activity
## GO:0043028 cysteine-type endopeptidase regulator activity involved in apoptotic process
##            GeneRatio  BgRatio       pvalue   p.adjust      qvalue geneID Count
## GO:0004998       1/4  2/18522 0.0004318838 0.01295651 0.004091531   TFRC     1
## GO:0120283       1/4  7/18522 0.0015109813 0.02266472 0.007157280   XIAP     1
## GO:0004707       1/4 16/18522 0.0034511548 0.03234409 0.010213925  MAPK3     1
## GO:0043027       1/4 20/18522 0.0043125460 0.03234409 0.010213925   XIAP     1
## GO:0004869       1/4 37/18522 0.0079672300 0.03961505 0.012510017   XIAP     1
## GO:0043028       1/4 42/18522 0.0090402197 0.03961505 0.012510017   XIAP     1
##                    ID
## GO:0051054 GO:0051054
## GO:0032872 GO:0032872
## GO:0070302 GO:0070302
## GO:0051403 GO:0051403
## GO:0031098 GO:0031098
## GO:1902528 GO:1902528
##                                                                Description
## GO:0051054                    positive regulation of DNA metabolic process
## GO:0032872                     regulation of stress-activated MAPK cascade
## GO:0070302 regulation of stress-activated protein kinase signaling cascade
## GO:0051403                                   stress-activated MAPK cascade
## GO:0031098               stress-activated protein kinase signaling cascade
## GO:1902528                 regulation of protein linear polyubiquitination
##            GeneRatio   BgRatio       pvalue    p.adjust       qvalue
## GO:0051054       3/4 301/18888 1.584016e-05 0.003341572 0.0009517791
## GO:0032872       2/4  35/18888 1.996811e-05 0.003341572 0.0009517791
## GO:0070302       2/4  38/18888 2.358757e-05 0.003341572 0.0009517791
## GO:0051403       2/4  50/18888 4.106724e-05 0.004363395 0.0012428244
## GO:0031098       2/4  59/18888 5.732355e-05 0.004872502 0.0013878333
## GO:1902528       1/4   2/18888 4.235157e-04 0.020667597 0.0058867459
##                      geneID Count
## GO:0051054 MAPK3/FOXM1/TFRC     3
## GO:0032872      MAPK3/FOXM1     2
## GO:0070302      MAPK3/FOXM1     2
## GO:0051403      MAPK3/FOXM1     2
## GO:0031098      MAPK3/FOXM1     2
## GO:1902528             XIAP     1
##                    ID                      Description GeneRatio   BgRatio
## GO:1990712 GO:1990712 HFE-transferrin receptor complex       1/4   8/19894
## GO:0005769 GO:0005769                   early endosome       2/4 428/19894
## GO:0031143 GO:0031143                     pseudopodium       1/4  18/19894
##                 pvalue   p.adjust     qvalue     geneID Count
## GO:1990712 0.001607676 0.03855515 0.01902392       TFRC     1
## GO:0005769 0.002692287 0.03855515 0.01902392 MAPK3/TFRC     2
## GO:0031143 0.003614545 0.03855515 0.01902392      MAPK3     1
##                    ID
## GO:0004998 GO:0004998
## GO:0106310 GO:0106310
## GO:0004857 GO:0004857
## GO:0072341 GO:0072341
## GO:0004699 GO:0004699
## GO:0004674 GO:0004674
##                                                                               Description
## GO:0004998                                                  transferrin receptor activity
## GO:0106310                                                 protein serine kinase activity
## GO:0004857                                                      enzyme inhibitor activity
## GO:0072341                                                    modified amino acid binding
## GO:0004699 diacylglycerol-dependent, calcium-independent serine/threonine kinase activity
## GO:0004674                                       protein serine/threonine kinase activity
##            GeneRatio   BgRatio      pvalue   p.adjust     qvalue
## GO:0004998      1/12   2/18522 0.001295372 0.02813253 0.01429602
## GO:0106310      3/12 363/18522 0.001440011 0.02813253 0.01429602
## GO:0004857      3/12 389/18522 0.001756270 0.02813253 0.01429602
## GO:0072341      2/12 101/18522 0.001875154 0.02813253 0.01429602
## GO:0004699      1/12   3/18522 0.001942480 0.02813253 0.01429602
## GO:0004674      3/12 427/18522 0.002292264 0.02813253 0.01429602
##                      geneID Count
## GO:0004998             TFRC     1
## GO:0106310 PRKCD/AKT1/MAPK3     3
## GO:0004857  AKT1/XIAP/ANXA1     3
## GO:0072341       TYMS/ANXA1     2
## GO:0004699            PRKCD     1
## GO:0004674 PRKCD/AKT1/MAPK3     3
##                    ID                                            Description
## GO:1900182 GO:1900182 positive regulation of protein localization to nucleus
## GO:0051054 GO:0051054           positive regulation of DNA metabolic process
## GO:1900180 GO:1900180          regulation of protein localization to nucleus
## GO:0042119 GO:0042119                                  neutrophil activation
## GO:0032079 GO:0032079  positive regulation of endodeoxyribonuclease activity
## GO:0050900 GO:0050900                                    leukocyte migration
##            GeneRatio   BgRatio       pvalue     p.adjust       qvalue
## GO:1900182      4/12  94/18888 2.761675e-07 0.0003628840 0.0001293627
## GO:0051054      5/12 301/18888 7.184948e-07 0.0004720511 0.0001682791
## GO:1900180      4/12 144/18888 1.529511e-06 0.0005830354 0.0002078433
## GO:0042119      3/12  42/18888 2.218042e-06 0.0005830354 0.0002078433
## GO:0032079      2/12   4/18888 2.218552e-06 0.0005830354 0.0002078433
## GO:0050900      5/12 396/18888 2.771090e-06 0.0006068688 0.0002163395
##                                 geneID Count
## GO:1900182       PRKCD/AKT1/WWTR1/TFRC     4
## GO:0051054 PRKCD/AKT1/MAPK3/FOXM1/TFRC     5
## GO:1900180       PRKCD/AKT1/WWTR1/TFRC     4
## GO:0042119           PRKCD/PREX1/ANXA1     3
## GO:0032079                  PRKCD/AKT1     2
## GO:0050900  AKT1/MAPK3/PREX1/RET/ANXA1     5
##                    ID                 Description GeneRatio   BgRatio
## GO:0005769 GO:0005769              early endosome      4/12 428/19894
## GO:0016323 GO:0016323 basolateral plasma membrane      3/12 255/19894
## GO:0009925 GO:0009925       basal plasma membrane      3/12 286/19894
## GO:0045178 GO:0045178          basal part of cell      3/12 305/19894
## GO:0016328 GO:0016328     lateral plasma membrane      2/12  68/19894
##                  pvalue    p.adjust      qvalue               geneID Count
## GO:0005769 9.118026e-05 0.006291438 0.004894940 MAPK3/RET/TFRC/ANXA1     4
## GO:0016323 4.203296e-04 0.010255994 0.007979492     TFRC/CLDN7/ANXA1     3
## GO:0009925 5.875358e-04 0.010255994 0.007979492     TFRC/CLDN7/ANXA1     3
## GO:0045178 7.084455e-04 0.010255994 0.007979492     TFRC/CLDN7/ANXA1     3
## GO:0016328 7.431879e-04 0.010255994 0.007979492          CLDN7/ANXA1     2
##                    ID                              Description GeneRatio
## GO:0004674 GO:0004674 protein serine/threonine kinase activity      5/12
## GO:0004707 GO:0004707                      MAP kinase activity      2/12
## GO:0106310 GO:0106310           protein serine kinase activity      4/12
## GO:0035173 GO:0035173                  histone kinase activity      2/12
## GO:0030544 GO:0030544                    Hsp70 protein binding      2/12
## GO:0001618 GO:0001618                  virus receptor activity      2/12
##              BgRatio       pvalue     p.adjust       qvalue
## GO:0004674 427/18522 4.408109e-06 0.0003702811 0.0001484837
## GO:0004707  16/18522 4.594242e-05 0.0017757774 0.0007120912
## GO:0106310 363/18522 6.342062e-05 0.0017757774 0.0007120912
## GO:0035173  23/18522 9.661815e-05 0.0020289811 0.0008136265
## GO:0030544  51/18522 4.820265e-04 0.0080980457 0.0032473366
## GO:0001618  79/18522 1.153123e-03 0.0108811215 0.0043633570
##                                  geneID Count
## GO:0004674 MAPK9/MAPK3/CHEK1/CDK1/EEF2K     5
## GO:0004707                  MAPK9/MAPK3     2
## GO:0106310       MAPK9/MAPK3/CHEK1/CDK1     4
## GO:0035173                   CHEK1/CDK1     2
## GO:0030544                    CDK1/TFRC     2
## GO:0001618                    CDK1/TFRC     2
##                    ID                                   Description GeneRatio
## GO:0042770 GO:0042770 signal transduction in response to DNA damage      5/12
## GO:0051054 GO:0051054  positive regulation of DNA metabolic process      5/12
## GO:0010038 GO:0010038                         response to metal ion      5/12
## GO:0046686 GO:0046686                       response to cadmium ion      3/12
## GO:0071241 GO:0071241      cellular response to inorganic substance      4/12
## GO:0048308 GO:0048308                         organelle inheritance      2/12
##              BgRatio       pvalue     p.adjust       qvalue
## GO:0042770 188/18888 6.932499e-08 6.544279e-05 2.875163e-05
## GO:0051054 301/18888 7.184948e-07 3.391296e-04 1.489931e-04
## GO:0010038 360/18888 1.735716e-06 5.461720e-04 2.399551e-04
## GO:0046686  60/18888 6.569175e-06 1.550325e-03 6.811197e-04
## GO:0071241 229/18888 9.653169e-06 1.822518e-03 8.007049e-04
## GO:0048308  15/18888 3.867417e-05 5.215488e-03 2.291372e-03
##                                  geneID Count
## GO:0042770 RAD51/MAPK3/CHEK1/CDK1/FOXM1     5
## GO:0051054  RAD51/MAPK3/CDK1/FOXM1/TFRC     5
## GO:0010038  MAPK9/MAPK3/CDK1/EEF2K/TFRC     5
## GO:0046686             MAPK9/MAPK3/CDK1     3
## GO:0071241      RAD51/MAPK9/MAPK3/EEF2K     4
## GO:0048308                   MAPK3/CDK1     2
##                    ID                                    Description GeneRatio
## GO:0000781 GO:0000781                   chromosome, telomeric region      3/12
## GO:0000794 GO:0000794                   condensed nuclear chromosome      2/12
## GO:0097122 GO:0097122                         cyclin A2-CDK1 complex      1/12
## GO:0097125 GO:0097125                         cyclin B1-CDK1 complex      1/12
## GO:0099182 GO:0099182 presynaptic intermediate filament cytoskeleton      1/12
## GO:0098687 GO:0098687                             chromosomal region      3/12
##              BgRatio       pvalue   p.adjust      qvalue           geneID Count
## GO:0000781 173/19894 0.0001342138 0.01167660 0.007346439 RAD51/CHEK1/CDK1     3
## GO:0000794  81/19894 0.0010524418 0.02098545 0.013203187      RAD51/CHEK1     2
## GO:0097122   2/19894 0.0012060603 0.02098545 0.013203187             CDK1     1
## GO:0097125   2/19894 0.0012060603 0.02098545 0.013203187             CDK1     1
## GO:0099182   2/19894 0.0012060603 0.02098545 0.013203187            RAD51     1
## GO:0098687 402/19894 0.0015730314 0.02280896 0.014350462 RAD51/CHEK1/CDK1     3
##                    ID                              Description GeneRatio
## GO:0004674 GO:0004674 protein serine/threonine kinase activity      5/13
## GO:0004707 GO:0004707                      MAP kinase activity      2/13
## GO:0106310 GO:0106310           protein serine kinase activity      4/13
## GO:0035173 GO:0035173                  histone kinase activity      2/13
## GO:0030544 GO:0030544                    Hsp70 protein binding      2/13
## GO:0001618 GO:0001618                  virus receptor activity      2/13
##              BgRatio       pvalue     p.adjust       qvalue
## GO:0004674 427/18522 7.027626e-06 0.0005973482 0.0002589125
## GO:0004707  16/18522 5.426823e-05 0.0023063998 0.0009996779
## GO:0106310 363/18522 9.019385e-05 0.0024245997 0.0010509101
## GO:0035173  23/18522 1.140988e-04 0.0024245997 0.0010509101
## GO:0030544  51/18522 5.686647e-04 0.0096673002 0.0041901611
## GO:0001618  79/18522 1.359016e-03 0.0119278915 0.0051699839
##                                  geneID Count
## GO:0004674 MAPK9/MAPK3/CHEK1/CDK1/EEF2K     5
## GO:0004707                  MAPK9/MAPK3     2
## GO:0106310       MAPK9/MAPK3/CHEK1/CDK1     4
## GO:0035173                   CHEK1/CDK1     2
## GO:0030544                    CDK1/TFRC     2
## GO:0001618                    CDK1/TFRC     2
##                    ID                                   Description GeneRatio
## GO:0042770 GO:0042770 signal transduction in response to DNA damage      5/13
## GO:0051054 GO:0051054  positive regulation of DNA metabolic process      5/13
## GO:0010038 GO:0010038                         response to metal ion      5/13
## GO:0046686 GO:0046686                       response to cadmium ion      3/13
## GO:0071241 GO:0071241      cellular response to inorganic substance      4/13
## GO:0048308 GO:0048308                         organelle inheritance      2/13
##              BgRatio       pvalue     p.adjust       qvalue
## GO:0042770 188/18888 1.117445e-07 0.0001108506 5.069672e-05
## GO:0051054 301/18888 1.152338e-06 0.0005715598 2.613989e-04
## GO:0010038 360/18888 2.776478e-06 0.0009180888 4.198814e-04
## GO:0046686  60/18888 8.520614e-06 0.0021131124 9.664171e-04
## GO:0071241 229/18888 1.381094e-05 0.0027400908 1.253161e-03
## GO:0048308  15/18888 4.568487e-05 0.0064741987 2.960929e-03
##                                  geneID Count
## GO:0042770 RAD51/MAPK3/CHEK1/CDK1/FOXM1     5
## GO:0051054  RAD51/MAPK3/CDK1/FOXM1/TFRC     5
## GO:0010038  MAPK9/MAPK3/CDK1/EEF2K/TFRC     5
## GO:0046686             MAPK9/MAPK3/CDK1     3
## GO:0071241      RAD51/MAPK9/MAPK3/EEF2K     4
## GO:0048308                   MAPK3/CDK1     2
##                    ID                                    Description GeneRatio
## GO:0000781 GO:0000781                   chromosome, telomeric region      3/13
## GO:0000794 GO:0000794                   condensed nuclear chromosome      2/13
## GO:0097122 GO:0097122                         cyclin A2-CDK1 complex      1/13
## GO:0097125 GO:0097125                         cyclin B1-CDK1 complex      1/13
## GO:0099182 GO:0099182 presynaptic intermediate filament cytoskeleton      1/13
## GO:0098687 GO:0098687                             chromosomal region      3/13
##              BgRatio       pvalue   p.adjust      qvalue           geneID Count
## GO:0000781 173/19894 0.0001733635 0.01508262 0.009671858 RAD51/CHEK1/CDK1     3
## GO:0000794  81/19894 0.0012405114 0.02273367 0.014578152      RAD51/CHEK1     2
## GO:0097122   2/19894 0.0013065325 0.02273367 0.014578152             CDK1     1
## GO:0097125   2/19894 0.0013065325 0.02273367 0.014578152             CDK1     1
## GO:0099182   2/19894 0.0013065325 0.02273367 0.014578152            RAD51     1
## GO:0098687 402/19894 0.0020144506 0.02920953 0.018730857 RAD51/CHEK1/CDK1     3
##                    ID
## GO:0004998 GO:0004998
## GO:0120283 GO:0120283
## GO:0004707 GO:0004707
## GO:0043027 GO:0043027
## GO:0004869 GO:0004869
## GO:0043028 GO:0043028
##                                                                             Description
## GO:0004998                                                transferrin receptor activity
## GO:0120283                                      protein serine/threonine kinase binding
## GO:0004707                                                          MAP kinase activity
## GO:0043027 cysteine-type endopeptidase inhibitor activity involved in apoptotic process
## GO:0004869                               cysteine-type endopeptidase inhibitor activity
## GO:0043028 cysteine-type endopeptidase regulator activity involved in apoptotic process
##            GeneRatio  BgRatio       pvalue   p.adjust      qvalue geneID Count
## GO:0004998       1/4  2/18522 0.0004318838 0.01295651 0.004091531   TFRC     1
## GO:0120283       1/4  7/18522 0.0015109813 0.02266472 0.007157280   XIAP     1
## GO:0004707       1/4 16/18522 0.0034511548 0.03234409 0.010213925  MAPK3     1
## GO:0043027       1/4 20/18522 0.0043125460 0.03234409 0.010213925   XIAP     1
## GO:0004869       1/4 37/18522 0.0079672300 0.03961505 0.012510017   XIAP     1
## GO:0043028       1/4 42/18522 0.0090402197 0.03961505 0.012510017   XIAP     1
##                    ID
## GO:0051054 GO:0051054
## GO:0032872 GO:0032872
## GO:0070302 GO:0070302
## GO:0051403 GO:0051403
## GO:0031098 GO:0031098
## GO:1902528 GO:1902528
##                                                                Description
## GO:0051054                    positive regulation of DNA metabolic process
## GO:0032872                     regulation of stress-activated MAPK cascade
## GO:0070302 regulation of stress-activated protein kinase signaling cascade
## GO:0051403                                   stress-activated MAPK cascade
## GO:0031098               stress-activated protein kinase signaling cascade
## GO:1902528                 regulation of protein linear polyubiquitination
##            GeneRatio   BgRatio       pvalue    p.adjust       qvalue
## GO:0051054       3/4 301/18888 1.584016e-05 0.003341572 0.0009517791
## GO:0032872       2/4  35/18888 1.996811e-05 0.003341572 0.0009517791
## GO:0070302       2/4  38/18888 2.358757e-05 0.003341572 0.0009517791
## GO:0051403       2/4  50/18888 4.106724e-05 0.004363395 0.0012428244
## GO:0031098       2/4  59/18888 5.732355e-05 0.004872502 0.0013878333
## GO:1902528       1/4   2/18888 4.235157e-04 0.020667597 0.0058867459
##                      geneID Count
## GO:0051054 MAPK3/FOXM1/TFRC     3
## GO:0032872      MAPK3/FOXM1     2
## GO:0070302      MAPK3/FOXM1     2
## GO:0051403      MAPK3/FOXM1     2
## GO:0031098      MAPK3/FOXM1     2
## GO:1902528             XIAP     1
##                    ID                      Description GeneRatio   BgRatio
## GO:1990712 GO:1990712 HFE-transferrin receptor complex       1/4   8/19894
## GO:0005769 GO:0005769                   early endosome       2/4 428/19894
## GO:0031143 GO:0031143                     pseudopodium       1/4  18/19894
##                 pvalue   p.adjust     qvalue     geneID Count
## GO:1990712 0.001607676 0.03855515 0.01902392       TFRC     1
## GO:0005769 0.002692287 0.03855515 0.01902392 MAPK3/TFRC     2
## GO:0031143 0.003614545 0.03855515 0.01902392      MAPK3     1
barplot(ego_MF[[1]], title = "enrichGO, Molecular Function, \n 3-Fold CV, alpha = 0.5, Deviance")

barplot(ego_MF[[2]], title = "enrichGO, Molecular Function, \n 3-Fold CV, alpha = 0.5, C-Index")

barplot(ego_MF[[3]], title = "enrichGO, Molecular Function, \n 3-Fold CV, alpha = 1, Deviance")

barplot(ego_MF[[4]], title = "enrichGO, Molecular Function, \n 3-Fold CV, alpha = 1, C-Index")

#barplot(ego_MF[[5]], title = "enrichGO, Molecular Function, \n 5-Fold CV, alpha = 0.5, Deviance")
barplot(ego_MF[[5]], title = "enrichGO, Molecular Function, \n 5-Fold CV, alpha = 0.5, C-Index")

barplot(ego_MF[[6]], title = "enrichGO, Molecular Function, \n 5-Fold CV, alpha = 1, Deviance")

barplot(ego_MF[[7]], title = "enrichGO, Molecular Function, \n 5-Fold CV, alpha = 1, C-Index")

barplot(ego_MF[[8]], title = "enrichGO, Molecular Function, \n 10-Fold CV, alpha = 0.5, Deviance")

barplot(ego_MF[[9]], title = "enrichGO, Molecular Function, \n 10-Fold CV, alpha = 0.5, C-Index")

barplot(ego_MF[[10]], title = "enrichGO, Molecular Function, \n 10-Fold CV, alpha = 1, Deviance")

#barplot(ego_MF[[11]], title = "enrichGO, Molecular Function, \n 10-Fold CV, alpha = 1, C-Index")

barplot(ego_BP[[1]], title = "enrichGO, Biological Process, \n 3-Fold CV, alpha = 0.5, Deviance")

barplot(ego_BP[[2]], title = "enrichGO, Biological Process, \n 3-Fold CV, alpha = 0.5, C-Index")

barplot(ego_BP[[3]], title = "enrichGO, Biological Process, \n 3-Fold CV, alpha = 1, Deviance")

barplot(ego_BP[[4]], title = "enrichGO, Biological Process, \n 3-Fold CV, alpha = 1, C-Index")

#barplot(ego_BP[[5]], title = "enrichGO, Biological Process, \n 5-Fold CV, alpha = 0.5, Deviance")
barplot(ego_BP[[5]], title = "enrichGO, Biological Process, \n 5-Fold CV, alpha = 0.5, C-Index")

barplot(ego_BP[[6]], title = "enrichGO, Biological Process, \n 5-Fold CV, alpha = 1, Deviance")

barplot(ego_BP[[7]], title = "enrichGO, Biological Process, \n 5-Fold CV, alpha = 1, C-Index")

barplot(ego_BP[[8]], title = "enrichGO, Biological Process, \n 10-Fold CV, alpha = 0.5, Deviance")

barplot(ego_BP[[9]], title = "enrichGO, Biological Process, \n 10-Fold CV, alpha = 0.5, C-Index")

barplot(ego_BP[[10]], title = "enrichGO, Biological Process, \n 10-Fold CV, alpha = 1, Deviance")

#barplot(ego_BP[[11]], title = "enrichGO, Biological Process, \n 10-Fold CV, alpha = 1, C-Index")

barplot(ego_CC[[1]], title = "enrichGO, Cellular Component, \n 3-Fold CV, alpha = 0.5, Deviance")

barplot(ego_CC[[2]], title = "enrichGO, Cellular Component, \n 3-Fold CV, alpha = 0.5, C-Index")

barplot(ego_CC[[3]], title = "enrichGO, Cellular Component, \n 3-Fold CV, alpha = 1, Deviance")

barplot(ego_CC[[4]], title = "enrichGO, Cellular Component, \n 3-Fold CV, alpha = 1, C-Index")

#barplot(ego_CC[[5]], title = "enrichGO, Cellular Component, \n 5-Fold CV, alpha = 0.5, Deviance")
barplot(ego_CC[[5]], title = "enrichGO, Cellular Component, \n 5-Fold CV, alpha = 0.5, C-Index")

barplot(ego_CC[[6]], title = "enrichGO, Cellular Component, \n 5-Fold CV, alpha = 1, Deviance")

barplot(ego_CC[[7]], title = "enrichGO, Cellular Component, \n 5-Fold CV, alpha = 1, C-Index")

barplot(ego_CC[[8]], title = "enrichGO, Cellular Component, \n 10-Fold CV, alpha = 0.5, Deviance")

barplot(ego_CC[[9]], title = "enrichGO, Cellular Component, \n 10-Fold CV, alpha = 0.5, C-Index")

barplot(ego_CC[[10]], title = "enrichGO, Cellular Component, \n 10-Fold CV, alpha = 1, Deviance")

#barplot(ego_CC[[11]], title = "enrichGO, Cellular Component, \n 10-Fold CV, alpha = 1, C-Index")

DAG plots for ego

goplot(ego_MF[[1]]) + labs(title = "enrichGO, Molecular Function, \n 3-Fold CV, alpha = 0.5, Deviance")

goplot(ego_MF[[2]]) + labs(title = "enrichGO, Molecular Function, \n 3-Fold CV, alpha = 0.5, C-Index")

goplot(ego_MF[[3]]) + labs(title = "enrichGO, Molecular Function, \n 3-Fold CV, alpha = 1, Deviance")

goplot(ego_MF[[4]]) + labs(title = "enrichGO, Molecular Function, \n 3-Fold CV, alpha = 1, C-Index")

#goplot(ego_MF[[5]]) + labs(title = "enrichGO, Molecular Function, \n 5-Fold CV, alpha = 0.5, Deviance")
goplot(ego_MF[[5]]) + labs(title = "enrichGO, Molecular Function, \n 5-Fold CV, alpha = 0.5, C-Index")

goplot(ego_MF[[6]]) + labs(title = "enrichGO, Molecular Function, \n 5-Fold CV, alpha = 1, Deviance")

goplot(ego_MF[[7]]) + labs(title = "enrichGO, Molecular Function, \n 5-Fold CV, alpha = 1, C-Index")

goplot(ego_MF[[8]]) + labs(title = "enrichGO, Molecular Function, \n 10-Fold CV, alpha = 0.5, Deviance")

goplot(ego_MF[[9]]) + labs(title = "enrichGO, Molecular Function, \n 10-Fold CV, alpha = 0.5, C-Index")

goplot(ego_MF[[10]]) + labs(title = "enrichGO, Molecular Function, \n 10-Fold CV, alpha = 1, Deviance")

#goplot(ego_MF[[11]]) + labs(title = "enrichGO, Molecular Function, \n 10-Fold CV, alpha = 1, C-Index")

goplot(ego_BP[[1]]) + labs(title = "enrichGO, Biological Process, \n 3-Fold CV, alpha = 0.5, Deviance")
## Warning: ggrepel: 2 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps

goplot(ego_BP[[2]]) + labs(title = "enrichGO, Biological Process, \n 3-Fold CV, alpha = 0.5, C-Index")
## Warning: ggrepel: 9 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps

goplot(ego_BP[[3]]) + labs(title = "enrichGO, Biological Process, \n 3-Fold CV, alpha = 1, Deviance")
## Warning: ggrepel: 14 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps

goplot(ego_BP[[4]]) + labs(title = "enrichGO, Biological Process, \n 3-Fold CV, alpha = 1, C-Index")
## Warning: ggrepel: 14 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps

#goplot(ego_BP[[5]]) + labs(title = "enrichGO, Biological Process, \n 5-Fold CV, alpha = 0.5, Deviance")
goplot(ego_BP[[5]]) + labs(title = "enrichGO, Biological Process, \n 5-Fold CV, alpha = 0.5, C-Index")
## Warning: ggrepel: 40 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps

goplot(ego_BP[[6]]) + labs(title = "enrichGO, Biological Process, \n 5-Fold CV, alpha = 1, Deviance")
## Warning: ggrepel: 14 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps

goplot(ego_BP[[7]]) + labs(title = "enrichGO, Biological Process, \n 5-Fold CV, alpha = 1, C-Index")
## Warning: ggrepel: 8 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps

goplot(ego_BP[[8]]) + labs(title = "enrichGO, Biological Process, \n 10-Fold CV, alpha = 0.5, Deviance")
## Warning: ggrepel: 9 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps

goplot(ego_BP[[9]]) + labs(title = "enrichGO, Biological Process, \n 10-Fold CV, alpha = 0.5, C-Index")
## Warning: ggrepel: 9 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps

goplot(ego_BP[[10]]) + labs(title = "enrichGO, Biological Process, \n 10-Fold CV, alpha = 1, Deviance")
## Warning: ggrepel: 14 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps

#goplot(ego_BP[[11]]) + labs(title = "enrichGO, Biological Process, \n 10-Fold CV, alpha = 1, C-Index")

goplot(ego_CC[[1]]) + labs(title = "enrichGO, Cellular Component, \n 3-Fold CV, alpha = 0.5, Deviance")

goplot(ego_CC[[2]]) + labs(title = "enrichGO, Cellular Component, \n 3-Fold CV, alpha = 0.5, C-Index")

goplot(ego_CC[[3]]) + labs(title = "enrichGO, Cellular Component, \n 3-Fold CV, alpha = 1, Deviance")

goplot(ego_CC[[4]]) + labs(title = "enrichGO, Cellular Component, \n 3-Fold CV, alpha = 1, C-Index")

#goplot(ego_CC[[5]]) + labs(title = "enrichGO, Cellular Component, \n 5-Fold CV, alpha = 0.5, Deviance")
goplot(ego_CC[[5]]) + labs(title = "enrichGO, Cellular Component, \n 5-Fold CV, alpha = 0.5, C-Index")

goplot(ego_CC[[6]]) + labs(title = "enrichGO, Cellular Component, \n 5-Fold CV, alpha = 1, Deviance")

goplot(ego_CC[[7]]) + labs(title = "enrichGO, Cellular Component, \n 5-Fold CV, alpha = 1, C-Index")

goplot(ego_CC[[8]]) + labs(title = "enrichGO, Cellular Component, \n 10-Fold CV, alpha = 0.5, Deviance")

goplot(ego_CC[[9]]) + labs(title = "enrichGO, Cellular Component, \n 10-Fold CV, alpha = 0.5, C-Index")

goplot(ego_CC[[10]]) + labs(title = "enrichGO, Cellular Component, \n 10-Fold CV, alpha = 1, Deviance")

#goplot(ego_CC[[11]]) + labs(title = "enrichGO, Cellular Component, \n 10-Fold CV, alpha = 1, C-Index")

3. Export Pathway Analysis result to data

pathway = list("ggo_MF" = ggo_MF,
               "ggo_BP" = ggo_BP,
               "ggo_CC" = ggo_CC,
               "ego_MF" = ego_MF,
               "ego_BP" = ego_BP,
               "ego_CC" = ego_CC)

saveRDS(pathway, file = "data/out_pathway/pathways_glmnet_cox_1se.rds")